User Manual of LocalDi Version 1.5
Contents
1. Duforet Frebourg Michael G B Blum if you wish to use this software please cite the Following reference Non stationary patterns of Isolation by distance inferring measures of genetic friction Nicolas Duforet Frebourg Michael G B Blum arXiv 1209 5242 Correlation matrix in File Matrix dat 30 populations detected Position matrix in file positions dat Each population has 4 neighbours at a distance 0 100000 Friction Results will be averaged over posterior sampling and neighbors positions dat Open Creating the batch of parameters Simu 1 on 10 alpha 0 366081 lambda 0 010000 range 15 100000 Simu 2 on 10 alpha 0 413831 lambda 0 001000 range 15 100000 Simu 3 on 10 alpha 0 381998 lambda 0 010000 range 15 100000 Simu 4 on 10 alpha 0 381998 lambda 0 000100 range 14 536001 Simu 5 on 10 alpha 0 405872 lambda 0 000010 range 13 972001 Simu 6 on 10 alpha 0 405872 lambda 0 000100 range 13 972001 Simu 7 on 10 alpha 0 421789 lambda 0 000100 range 13 972001 Simu 8 on 10 alpha 0 381998 lambda 0 001000 range 13 408001 Simu 9 on 10 alpha 0 389956 lambda 0 010000 range 12 844000 Simu 10 on 10 alpha 0 413831 lambda 0 000010 range 12 844000 Writing results in LocalDiff res Results written Figure 1 the Graphical User Interface for LocalDiff 3 0 0 1 1 0 1 9 2 1 9 0 1 1 1 1 A matrix of larger dimension which is used in example 3 is provided in Examples GenoBarrier2D dat Positions All2. User Manual of LocalDiff Version 1 5 Nicolas Duforet Frebourg and Michael Blum Universit Joseph Fourier Centre National de la Recherche Scientifique Laboratoire TIMC IMAG Grenoble France December 2012 1 Introduction LocalDiff provides Bayesian measures of Local Genetic Differentiation to characterize non stationary patterns of isolation by distance Non stationary patterns of isolation by distance arise when genetic differentiation between populations or between individuals increases at different rates in differ ent regions of the habitat Typical patterns include barriers to gene flows secondary contact zone corridors for gene flow or gradients of gene flow across the habitat By analogy with the concept of LocalDiff map in ecol ogy which measures the cost of movement through the landscape LocalDiff provide estimates of Local Genetic Differentiation with larger Differentiation values indicating larger population genetic differentiation per unit of spatial distance 2 Algorithm The software draws a batch of parameter using a MCMC algorithm to char acterize decay of a pairwise statistic and then compute a posterior predictive value of Local Differentiation using equations in 2 3 Starters 3 1 Download An archive containing the software can be downloaded at the following web page http membres timc imag fr Michael Blum LocalDiff html 3 2 Windows OS If you are using windows 64 bits you can directly
3. a J Du Croz A Greenbaum S Hammarling A McKenney and D Sorensen LAPACK Users Guide Society for Industrial and Applied Mathematics Philadelphia PA third edition 1999 2 Blum M G B Duforet Frebourg N Non stationary patterns of isolation by distance inferring measures of genetic friction ArXiv mois 2012 3 R R Hudson Generating samples under a wright fisher neutral model of genetic variation Bioinformatics 18 2 337 338 2002 11
4. at Genotypes LocalDiff can also compute similarity measures from geno types and then use those measures in the algorithm This file must be a nsam x nbMarkers 1 matrix The first column corresponds to the population labels integers from 1 to n If a LabelFile is used the labels must be the position of the population label in the label file e g an individ ual with label 1 would be of the first population in the labelfile and so on The order of the individuals does not matter Missing values are handled and must be coded with the value 9 Correlation or Covariance of allele frequencies between population for SNP data are handled data can be either haploid e g 0 and 1 or Diploid 0 1 and 2 F st and other measures such as Identity By State will be available soon An example of genotype file is provided below Input file Matrix dat v Browse C Compute Pairwise Dissimilarity statistics Update your choice Pairwise File Fst Browse H ploSNP Positions positions dat v Browse Label file m Browse 7 F s Output file LocalDiff res v Browse C Use Great Circles distance Average results over neighbors and simulated parameters number of neighbors per site 4 Distance of the neighbors 1 number of replicates 10 frrremeennennenenneneeneneneenmentarenennnl Welcome to the Software LocalDiff SRARRARRRARERRRRERRRERERERERERRRAERERERER version 1 5 December 2012 Nicolas
5. can be euclidean coordinates or geographic coordinates longitudes and latitudes The dis tance_ type parameter must be chosen accordingly to the coordinate system The value can be euclidean for standard euclidean coordinates or great circle if positions are geographic coordinates Default value is euclidean 5 Graphical User Interface If you are not familiar with command line you may prefer the GUI program of the archive This Program is a simple friendly user interface that runs LocalDiff for you All the slots to fulfill correspond to arguments of the command line You can see for example figure To run the software correctly LocalDiff and the GUI must be in the same directory 6 Files 6 1 Input Files Similarity Matrix Estimates of LocalDiff measures can be computed for any type of pairwise measures of similarities between populations or indi viduals provided that they decrease with geographical distance Classical measures include the Pearson correlation one minus Fst values identity by state or by descent measures Whatever your choice of statistic the input file should be the same Each line of the input file corresponds to one row of the matrix and all features are separated by at least one blank An example of a 4 x 4 matrix is provided below 1 0 79 0 85 0 82 0 79 1 0 80 0 80 0 85 0 8 1 0 89 0 82 0 9 089 1 A matrix of larger dimension which is used in example 1 is provided in Examples Matrix1D d
6. ile Position1D dat contains the coordinates of those 30 populations A way to run LocalDiff here would be MyMachine gt LocalDiff i Examples Matrix1D dat p Examples PositioniD dat o Examples My1DResults n 2 0 1 s 200 To provide a LocalDiff map run R MyMachine gt R and in the R command line type gt source Rfiles Display1D R 8 2 Example 2 2 dimensionnal habitat with a gradient of migrations A stepping stone model was also used for the second example The habi tat is 2 dimensional habitat with a grid 10 x 10 populations There is no barrier to gene flow here but varying effective migration parameter which decreases from the south west to the north east We expect Local Genetic Differentiation to increase from the south west to the north east The file Matrix2DG dat contains the matrix of pairwise correlations of allele frequen cies between the 100 populations and the file Position1DG dat contains the coordinates of those 100 populations The command line for running LocalDiff is MyMachine gt LocalDiff i Examples Matrix2DG dat p Examples Position2DG dat o Examples My2DResults n 4 0 1 s 200 To provide a LocalDiff map run R MyMachine gt R and in the R command line type gt source Rfiles Display2D R 8 3 Example 2 2 dimensionnal habitat with 2 barriers to gene flows A stepping stone model was also used for the second example The habitat is 2 dimensional habitat with a grid 10 x 10 po
7. ile datatype i INPUTFile p PositionFile o OUTPUTFile l LabelFile n number_of_neighbors distance_to_neighbors s number_of_posterior_replicates m doMean v verbose d distance_type i INPUTFile The input file is the name with the path of the file con taining the pairwise matrix of correlation or any other relevant pairwise measure you want to estimate locally c genetic Measure MatrixFile datatype LocalDiff can also handle files of genotypes such as Structure s input files and compute genetic mea sures of similarity the first parameter genetic_ Measure tells which measure to compute it can be Cov Cor for Covariance or Correlation of allele fre quencies between populations Fst for Fst measures as described by Weir and Cockerham between populations The second parameter tells where to write the calculated matrix datatype tells what kind of data is in the file it is either HaploSNP DiploSNP or MultiAllelic for Microsatellites or others WARNING if you use this option c is the first parameter you must specify such as example 3 p PositionFile The position file gives the coordinates of all sampled pop ulations or individuals The positions can either be Cartesian coordinates or the longitude and the latitude of the sampling sites longitude should be the first coordinate 0 OUTPUTFile The output file is the name and path you want to give to the output file which contains the locations and LocalDiff values for all samp
8. istics So you can use LocalDiff as a quick way to compute Statistic on your data 7 Displaying the results with a Local Genetic Dif ferentiation map 7 1 Advocated tools LocalDiff does not provide any visualization tool for displaying Local Genetic Differentiation map Thus the software remains really easy to use on any gt myLocalDiffRun lo computer without calling graphical libraries Displaying a Local Genetic Differentiation map after a run of LocalDiff can be performed with the R software and the packages spl and A possibility is to display a map of LocalDiff values using a grid that spans the range of the data This is done by using another layer of Kriging in a much more classical way this time How to display the results with R is shown afterwards for two different examples 8 Examples 8 1 Example 1 1 dimensionnal habitat with a barrier In the Example repertory of the archive LocalDiff tar gz we provide files to run LocalDiff on a first simple example The data were simulated using the software ms 3 We assume that 30 populations evolved according to a classical stepping stone model Five units of coalescent ago a barrier to gene flow arose between populations 15 and 16 Because of the barrier to gene flow we expect larger Local Genetic Differentiation measures for populations 15 and 16 The file Matrix1D dat contains the matrix of pairwise correlations of allele frequencies between the 30 populations and the f
9. les sites l LabelFile The label file may not be specified It contains the name of the sampled populations or individuals of the data set Default labels are popl pop2 popn n number_of_ neighbors distance to neighbors Here are speci fied the parameters that define the neighborhoods The first parameter is the number of fictive neighboring populations in the vicinity of each sam pled site The second parameter is the distance between the neighbors and the sampling site The unit for the distance corresponds to the Euclidean distance when using Cartesian coordinates and is in kilometer when using longitude and latitude By default we consider 2 neighbors and we use a distance between neighbors and sampling sites equal to one tenth of the minimum distance between sampling sites s number of posterior replicates Estimates of LocalDiff measures are averaged over posterior replicates of the parameters of the correlogram model By default the number of posterior replicates is equal to 100 m doMean Set this parameter to 1 if you wish LocalDiff values averaged over unsampled sites and over replicates of the posterior distribution If however you wish the detail of those values you can set this parameter to 0 Default value is 1 v verbose This parameter specifies the level of details to output from the execution the parameter is an integer between 0 1 or 2 Default value is 1 d distance type The coordinates in the PositionFile
10. pulations 2 barriers to gene flow are present here one between x 5 and x 6 at T 5 The other one between y 7 and y 6 x gt 5 at T 3 We expect Local Genetic Differentiation to reveal those two barriers The file GenoBarrier2D dat contains the matrix of genotypes of individuals from 100 populations and the file Position1DG dat contains the coordinates of those 100 populations The command lien for running LocalDiff is MyMachine gt LocalDiff c Cor Examples CorrelationMatrix HaploSNP i Examples GenoBarrier2D dat p Examples Position2DG dat o Examples My2DResults_2 n 4 0 1 s 200 To provide a LocalDiff map run R MyMachine gt R and in the R command line type gt source Rfiles Display2D_2 R 8 4 More detailed plots Raster file If you want to display the LocalDiff map on a specific region only you can use a raster file for that An example of a raster file for display ing the locations above 1 000 meters is given Generating a LocalDiff map with this raster can be performed by sourcing the file DisplayFromascFile R in R Administrative Area If your habitat corresponds to an administrative zone country county city you can use the global administration ar to restrict the fircion map to the region of interest How to display the LocalDiff map for the human Swedish sample is shown in DisplayFromgadmPolygon R 10 References 1 E Anderson Z Bai C Bischof S Blackford J Demmel J Don garr
11. responds to the name of the population the two coordinates and finally the mean Local Genetic Differentiation In the case of a detailed output m 0 this output file is an array of dimensions n X nu X Nsimu 4 where n is the number of sampled popu lation n is the number of unsampled neighbors by population and Nsimu is the number of parameters simulated Each row corresponds to one unsam pled population The first column is the name of the sampled population whom the unsampled population is the neighbor The second column is the index of this neighbor for the sampled population Columns three and four are the coordinates in the habitat of this neighbor Then the remaining nsimu columns are the LocalDiff values one for each value of parameter simulated You may want to mean over those values to obtain one Local Genetic Dif ferentiation value per unsampled population but you can also observe other statistics A typical output file with no labels would look like popl 1 0 9 1 0 012 popl 2 1 1 1 0 013 pop2 1 1 9 1 0 014 Note save a logfile Note that if you wish to save a journal of the run you can still redirect the flow in a log file typing MyMachine gt LocalDiff Note using c If you are using the pairwise statistic calculation on geno typic data Ft Correlations or Covariances you will have a second output file This file is the second argument of the c option and contain the matrix of pairwise stat
12. sampled sites Populations or individuals should be geo referenced must have an associated geographical Site The coordinates can either be Cartesian coordinates or geographic coordinates longitude followed by latitude Each line of the file corresponds to one sampling site with its associates coordinates If you are using longitude and latitude the order matters and longitude must be specified first Beware the software checks for number of sites and number of individuals populations in the matrix to be the same If they are different the program stops with the following message The Number of populations in the position file does not correspond to the dimension of the input matrix An example with 4 sampling sites is provided below ee ee NB NH The position file of example is provided in Examples Position1D dat Labels The Label file is an optional input file It gives names to indi viduals populations of your dataset to be printed in the output files If no name is mentioned default names would be popi pop2 To complete the previous example with 4 sampling sites an appropriate Label file could be Michael Sean Eric Olivier 6 2 Output File For the sack of simplicity there is only one output file after a run of LocalDiff Its name is specified by the o parameter If one average over replicates and neighbors this file is a n x 4 array Every line of the array describes one samples site The four columns cor
13. use the software LocalDiff exe The first one is the command line software You will have to open a ter minal first run then type cmd Then go in the repertory containing the executable file LocalDiff exe and just type LocalDiff exe with the pa rameters of your choice 3 3 UNIX OS Extraction and Compilation The archive of the program is provided with a Makefile for UNIX OS Compilation proceeds as follows First you need to compile the local modified Lapack library MyMachine gt make lapack Then compile the program MyMachine gt make After compilation if for some reasons you want to clean the repertory of all executables and binary files including Lapack objects just type MyMachine gt make realclean If you want to remove all executables and binary files but Lapack objects just type MyMachine gt make clean After compilation you can run the program You can run it without parameters and a presentation screen will be displayed Then the software is run as other usual software for LINUX 3 4 MAC OS The software has been initially developped for UNIX type of Operating sys tem It should be running fine with MAC OS 4 Command line Here is a complete list of the parameters of the program and their meaning When a parameter can be unspecified it is explicitly mentioned Basically the command line to run the software is the following one MyMachine gt LocalDiff c genetic_Measure MatrixF
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